2-(Pyridin-4-yl)-1H-benzimidazole

Geiger, D.K.; Bond, C.J.

doi:10.1107/S160053681301252X

organic compounds

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ISSN: 2056-9890

Volume 69| Part 6| June 2013| Page o869

doi:10.1107/S160053681301252X

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2-(Pyridin-4-yl)-1H-benzimidazole

David K. Geiger ^a ^* and Christopher J. Bond ^a

^aDepartment of Chemistry, State University of New York-College at Geneseo, 1 College Circle, Geneseo, NY 14454, USA
^*Correspondence e-mail: geiger@geneseo.edu

(Received 16 April 2013; accepted 7 May 2013; online 11 May 2013)

The title compound, C₁₂H₉N₃, is an unhydrated analogue of the previously reported trihydrate. The molecule is essentially planar, with a 3.62 (11)° angle between the pyridine and benzimidazole planes. In the crystal, N—H⋯N hydrogen bonds result in chains of molecules parallel to [010], which are additionally linked by weak π–π stacking interactions [centroid–centroid distance = 3.7469 (17) Å], resulting in extended sheets of molecules parallel to (103).

Related literature

For the structure of the trihydrate of the title compound, see: Huang et al. (2004 )

Experimental

Crystal data

C₁₂H₉N₃
M_r = 195.22
Monoclinic, P 2₁ /n
a = 6.0602 (14) Å
b = 11.610 (3) Å
c = 13.892 (4) Å
β = 101.838 (8)°
V = 956.6 (4) Å³
Z = 4
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 200 K
0.50 × 0.20 × 0.20 mm

Data collection

Bruker SMART X2S CCD diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2010 ) T_min = 0.53, T_max = 0.98
4809 measured reflections
1699 independent reflections
1125 reflections with I > 2σ(I)
R_int = 0.058

Refinement

R[F² > 2σ(F²)] = 0.046
wR(F²) = 0.128
S = 0.96
1699 reflections
140 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.26 e Å⁻³
Δρ_min = −0.25 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯N3ⁱ	0.99 (2)	1.96 (2)	2.924 (2)	165 (2)
Symmetry code: (i) $[-x+{\script{3\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Data collection: APEX2 (Bruker, 2010); cell refinement: SAINT (Bruker, 2010); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009 ) and Mercury (Macrae et al., 2008 ); software used to prepare material for publication: publCIF (Westrip, 2010 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S160053681301252X/im2430sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S160053681301252X/im2430Isup2.hkl

Supporting information file. DOI: 10.1107/S160053681301252X/im2430Isup3.mol

Supporting information file. DOI: 10.1107/S160053681301252X/im2430Isup4.cml

checkCIF report

Comment top

Single crystals of the title compound were obtained by slow evaporation of an ethylacetate solution.

Figure 1 shows a perspective view of the title compound with the atom numbering scheme. The non-hydrogen atoms of the molecule are essentially planar with a r. m. s. deviation of 0.0308 Å. The maximum deviation is 0.0480 (18) Å for C12. The pyridine and benzimidazole planes exhibit a dihedral angle of 3.62 (11)°, which is similar to the value (2.8 (1)°) reported for the trihydrate analogue (Huang et al., 2004).

Hydrogen-bonding interactions involving the benzimidazole N—H and the pyridine result in chains of molecules parallel to [0 1 0]. Figure 2 shows a packing diagram with the hydrogen-bonded chains displayed. The trihydrate (Huang et al., 2004) hydrogen-bonding network is much more extensive, involving the three waters of hydration, the benzimidazole amine group and the pyridine. As seen in figure 2, pairs of molecules related by an inversion center exhibit π stacking. The spacing between the mean planes formed by the molecules is 3.43 Å. The shortest internuclear separation between related molecules is 3.460 (2) Å (N2···C7).

Related literature top

For the structure of the trihydrate of the title compound, see: Huang et al. (2004)

Experimental top

The title compound was prepared by stirring 0.373 g (3.45 mmole) o-phenylenediamine, 0.67 ml (7.1 mmole) 4-pyridinecarboxaldehyde, and 0.75 g NH₄Cl in 25 ml CHCl₃ for 5 days at room temperature. After removal of the solvent, the crude product mixture was extracted with water and ethylacetate and the solvent was removed from the organic phase. The resulting solid was passed through a short silica column using a 30:70 mixture of hexanes: ethyl acetate, yielding 0.442 g of solid that contained two components based on TLC analysis was obtained. The mixture was passed through a second silica column using 90:10 ethyl acetate: ethanol. The first component isolated was the title compound (0.380 g, 1.95 mmole, 56% yield). ¹H NMR (400 MHz, DMSO-d₆): δ, 7.27 (m, 2H), 7.64 (m, 2H), 8.09 (d, 2H), 8.75, (d, 2H). ¹³C NMR (DMSO-d₆): δ, 120.89, 123.52, 137.77, 149.06, 150.67, 163.55.

Computing details top

Data collection: APEX2 (Bruker, 2010); cell refinement: SAINT (Bruker, 2010); data reduction: SAINT (Bruker, 2010); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009) and Mercury (Macrae et al., 2008); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top

	Fig. 1. Perspective view of the title compound. Thermal parameters are drawn at the 50% probability level.
	Fig. 2. Packing diagram down [1 0 0] displaying the H-bonding network.

2-(Pyridin-4-yl)-1H-benzimidazole top

Crystal data top

C₁₂H₉N₃	F(000) = 408
M_r = 195.22	D_x = 1.356 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
a = 6.0602 (14) Å	Cell parameters from 1098 reflections
b = 11.610 (3) Å	θ = 2.3–24.2°
c = 13.892 (4) Å	µ = 0.09 mm⁻¹
β = 101.838 (8)°	T = 200 K
V = 956.6 (4) Å³	Prism, clear yellow
Z = 4	0.50 × 0.20 × 0.20 mm

Data collection top

Bruker SMART X2S CCD diffractometer	1699 independent reflections
Radiation source: XOS X-beam microfocus source	1125 reflections with I > 2σ(I)
Doubly curved silicon crystal monochromator	R_int = 0.058
Detector resolution: 8.3330 pixels mm^-1	θ_max = 25.4°, θ_min = 3.0°
ω scans	h = −7→7
Absorption correction: multi-scan (SADABS; Bruker, 2010)	k = −13→8
T_min = 0.53, T_max = 0.98	l = −16→16
4809 measured reflections

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.046	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.128	H atoms treated by a mixture of independent and constrained refinement
S = 0.96	w = 1/[σ²(F_o²) + (0.0664P)²] where P = (F_o² + 2F_c²)/3
1699 reflections	(Δ/σ)_max < 0.001
140 parameters	Δρ_max = 0.26 e Å⁻³
0 restraints	Δρ_min = −0.25 e Å⁻³

Crystal data top

C₁₂H₉N₃	V = 956.6 (4) Å³
M_r = 195.22	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 6.0602 (14) Å	µ = 0.09 mm⁻¹
b = 11.610 (3) Å	T = 200 K
c = 13.892 (4) Å	0.50 × 0.20 × 0.20 mm
β = 101.838 (8)°

Data collection top

Bruker SMART X2S CCD diffractometer	1699 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2010)	1125 reflections with I > 2σ(I)
T_min = 0.53, T_max = 0.98	R_int = 0.058
4809 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.046	0 restraints
wR(F²) = 0.128	H atoms treated by a mixture of independent and constrained refinement
S = 0.96	Δρ_max = 0.26 e Å⁻³
1699 reflections	Δρ_min = −0.25 e Å⁻³
140 parameters

Special details top

Experimental. The H atoms bonded to carbon were refined using a riding model with C—H = 0.95 Å and U_iso = 1.2U_eq(C). The coordinates and isotropic thermal parameters of the amine H atom were refined freely.

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
N1	0.4979 (3)	0.67895 (13)	0.38292 (14)	0.0331 (5)
H1	0.618 (4)	0.7118 (19)	0.3528 (19)	0.062 (7)*
N2	0.2493 (3)	0.54899 (13)	0.41681 (13)	0.0303 (5)
N3	0.7075 (3)	0.30522 (13)	0.22238 (14)	0.0357 (5)
C1	0.3669 (3)	0.73593 (15)	0.43732 (16)	0.0294 (5)
C2	0.2130 (3)	0.65460 (15)	0.45835 (16)	0.0286 (5)
C3	0.0506 (3)	0.68515 (17)	0.51158 (17)	0.0338 (6)
H3	−0.0548	0.6305	0.5259	0.041*
C4	0.0490 (3)	0.79775 (16)	0.54271 (18)	0.0389 (6)
H4	−0.0594	0.8211	0.5794	0.047*
C5	0.2039 (3)	0.87851 (17)	0.52133 (19)	0.0412 (6)
H5	0.1968	0.9556	0.5434	0.049*
C6	0.3650 (4)	0.84967 (16)	0.46965 (18)	0.0398 (6)
H6	0.471	0.9046	0.4563	0.048*
C7	0.4191 (3)	0.56767 (15)	0.37324 (16)	0.0284 (5)
C8	0.5194 (3)	0.47905 (15)	0.32041 (16)	0.0295 (5)
C9	0.7077 (4)	0.49937 (16)	0.28180 (18)	0.0368 (6)
H9	0.7769	0.5732	0.2878	0.044*
C10	0.7947 (4)	0.41118 (17)	0.23429 (18)	0.0395 (6)
H10	0.9251	0.4268	0.2084	0.047*
C11	0.5260 (3)	0.28667 (16)	0.26116 (17)	0.0352 (6)
H11	0.4609	0.2119	0.2545	0.042*
C12	0.4278 (3)	0.36867 (15)	0.30996 (17)	0.0336 (6)
H12	0.2992	0.3503	0.3362	0.04*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
N1	0.0314 (10)	0.0239 (9)	0.0474 (13)	−0.0038 (7)	0.0161 (9)	−0.0026 (8)
N2	0.0291 (10)	0.0267 (9)	0.0376 (12)	−0.0014 (7)	0.0130 (9)	0.0002 (7)
N3	0.0372 (11)	0.0305 (9)	0.0406 (13)	0.0062 (8)	0.0110 (9)	−0.0012 (8)
C1	0.0284 (11)	0.0270 (10)	0.0342 (14)	0.0005 (8)	0.0098 (10)	−0.0002 (9)
C2	0.0270 (11)	0.0259 (10)	0.0334 (13)	−0.0006 (8)	0.0075 (10)	0.0002 (9)
C3	0.0296 (12)	0.0350 (11)	0.0381 (15)	−0.0014 (9)	0.0104 (11)	0.0019 (9)
C4	0.0375 (13)	0.0379 (12)	0.0454 (16)	0.0028 (10)	0.0182 (12)	−0.0031 (10)
C5	0.0478 (14)	0.0292 (11)	0.0501 (16)	−0.0011 (9)	0.0185 (12)	−0.0083 (10)
C6	0.0426 (14)	0.0274 (11)	0.0519 (17)	−0.0073 (9)	0.0158 (12)	−0.0059 (10)
C7	0.0261 (11)	0.0242 (10)	0.0353 (14)	−0.0011 (8)	0.0074 (10)	0.0010 (9)
C8	0.0279 (12)	0.0241 (9)	0.0362 (14)	0.0036 (8)	0.0056 (10)	0.0019 (9)
C9	0.0380 (13)	0.0252 (10)	0.0511 (17)	−0.0010 (9)	0.0183 (12)	0.0008 (9)
C10	0.0374 (13)	0.0362 (11)	0.0496 (16)	0.0028 (9)	0.0201 (12)	0.0032 (10)
C11	0.0339 (13)	0.0276 (10)	0.0450 (16)	0.0005 (9)	0.0105 (11)	−0.0047 (9)
C12	0.0297 (12)	0.0293 (11)	0.0437 (15)	−0.0021 (9)	0.0119 (11)	−0.0013 (9)

Geometric parameters (Å, º) top

N1—C1	1.373 (3)	C4—H4	0.95
N1—C7	1.374 (2)	C5—C6	1.367 (3)
N1—H1	0.99 (2)	C5—H5	0.95
N2—C7	1.315 (3)	C6—H6	0.95
N2—C2	1.392 (2)	C7—C8	1.466 (3)
N3—C10	1.336 (2)	C8—C9	1.377 (3)
N3—C11	1.338 (3)	C8—C12	1.392 (3)
C1—C6	1.396 (3)	C9—C10	1.380 (3)
C1—C2	1.399 (3)	C9—H9	0.95
C2—C3	1.393 (3)	C10—H10	0.95
C3—C4	1.378 (3)	C11—C12	1.373 (3)
C3—H3	0.95	C11—H11	0.95
C4—C5	1.401 (3)	C12—H12	0.95

C1—N1—C7	106.18 (16)	C5—C6—H6	121.5
C1—N1—H1	127.4 (13)	C1—C6—H6	121.5
C7—N1—H1	126.4 (14)	N2—C7—N1	113.51 (17)
C7—N2—C2	104.53 (15)	N2—C7—C8	123.97 (16)
C10—N3—C11	115.83 (18)	N1—C7—C8	122.52 (18)
N1—C1—C6	132.60 (19)	C9—C8—C12	117.48 (19)
N1—C1—C2	105.96 (16)	C9—C8—C7	122.43 (17)
C6—C1—C2	121.44 (19)	C12—C8—C7	120.06 (19)
N2—C2—C3	129.31 (18)	C8—C9—C10	119.18 (18)
N2—C2—C1	109.83 (18)	C8—C9—H9	120.4
C3—C2—C1	120.84 (18)	C10—C9—H9	120.4
C4—C3—C2	117.37 (19)	N3—C10—C9	124.2 (2)
C4—C3—H3	121.3	N3—C10—H10	117.9
C2—C3—H3	121.3	C9—C10—H10	117.9
C3—C4—C5	121.4 (2)	N3—C11—C12	124.24 (18)
C3—C4—H4	119.3	N3—C11—H11	117.9
C5—C4—H4	119.3	C12—C11—H11	117.9
C6—C5—C4	121.96 (19)	C11—C12—C8	119.1 (2)
C6—C5—H5	119.0	C11—C12—H12	120.5
C4—C5—H5	119.0	C8—C12—H12	120.5
C5—C6—C1	117.04 (19)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···N3ⁱ	0.99 (2)	1.96 (2)	2.924 (2)	165 (2)

Symmetry code: (i) −x+3/2, y+1/2, −z+1/2.

Experimental details

Crystal data
Chemical formula	C₁₂H₉N₃
M_r	195.22
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	200
a, b, c (Å)	6.0602 (14), 11.610 (3), 13.892 (4)
β (°)	101.838 (8)
V (Å³)	956.6 (4)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.09
Crystal size (mm)	0.50 × 0.20 × 0.20

Data collection
Diffractometer	Bruker SMART X2S CCD diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2010)
T_min, T_max	0.53, 0.98
No. of measured, independent and observed [I > 2σ(I)] reflections	4809, 1699, 1125
R_int	0.058
(sin θ/λ)_max (Å⁻¹)	0.603

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.046, 0.128, 0.96
No. of reflections	1699
No. of parameters	140
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.26, −0.25

Computer programs: APEX2 (Bruker, 2010), SAINT (Bruker, 2010), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2009) and Mercury (Macrae et al., 2008), publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···N3ⁱ	0.99 (2)	1.96 (2)	2.924 (2)	165 (2)

Symmetry code: (i) −x+3/2, y+1/2, −z+1/2.

Acknowledgements

This work was supported by a Congressionally directed grant from the US Department of Education (grant No. P116Z100020) for the X-ray diffractometer.

References

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